GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Halococcus hamelinensis 100A6

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_007694083.1 C447_RS11620 class II fructose-bisphosphate aldolase

Query= BRENDA::D4GYE0
         (330 letters)



>NCBI__GCF_000336675.1:WP_007694083.1
          Length = 336

 Score =  301 bits (770), Expect = 2e-86
 Identities = 153/326 (46%), Positives = 221/326 (67%), Gaps = 8/326 (2%)

Query: 8   ELATVYDEALDEGFGLIASNIAEPNIMMGLMEGADRMDSDLLLQMSGGACRFAGDGDAVA 67
           +L  +Y+ A    +G  ASN+ + ++++GL++G+   D+DL++Q S     F G GD   
Sbjct: 10  DLRELYERARAGRYGFFASNVTQFDVLVGLLDGSAAADADLVVQASREEAAFFGGGDPTV 69

Query: 68  GLKAMGNYIETIAERYDIGVFLNMDH---QTDLEFIEQQIELDIPSSIMIDASHEPFDEN 124
           GL+ +G  ++++A+RY I  F N+DH     +  F+E  ++ D+P S+M+DAS  PF+EN
Sbjct: 70  GLEVLGAALDSLADRYGIEAFCNVDHVHLPEEQSFLETCLDSDVPDSVMVDASDRPFEEN 129

Query: 125 VATSREVVEMVEAAGSDVLIEAELGQIKGVEDEIE--AEEAFYTDPEQAVEFVDKTGADL 182
           V  + E VE    A  DVL+EAELG+I GVE   E  A+EAFYTDP  AVEFV++TG DL
Sbjct: 130 VELTAETVER---ADDDVLVEAELGRIAGVEGSTETAADEAFYTDPGTAVEFVERTGCDL 186

Query: 183 LAISVGTQHGVAKGKDLELRPDLANDIRQALRDHGLDTPLVLHGSSGVQPDQLQEMLKHG 242
           LA+S+GTQHGVA  +DL++RPDLA  I +AL + G +T LV+HG+SG+  ++++ +L  G
Sbjct: 187 LAVSIGTQHGVASDRDLDVRPDLAVAIDEALVEAGEETFLVVHGASGLADERIEALLDAG 246

Query: 243 ICKVNKDTRYQYEYTRTAYDRYNEEPNAIVPPEGVADARDTFFNETDWSPNKDVFDPRVA 302
           +CK NK+TRYQYE+ RTA D Y++  +AI PPEGV D R  FF  +DWSP K  F P V 
Sbjct: 247 VCKFNKNTRYQYEFARTAADFYHDHADAIRPPEGVPDDRSNFFAGSDWSPEKASFHPHVV 306

Query: 303 GRDIRERIADVHADLTEVSGSAGQSL 328
               R RIA V ++L EV+G+AG+++
Sbjct: 307 SNAARNRIATVMSELCEVTGNAGETM 332


Lambda     K      H
   0.315    0.135    0.384 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 390
Number of extensions: 13
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 330
Length of database: 336
Length adjustment: 28
Effective length of query: 302
Effective length of database: 308
Effective search space:    93016
Effective search space used:    93016
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory